Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009171.1 Kokia drynarioides strain JFW-HI SEQ_123876, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 10839
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:1546 original size:17 final size:17

Alignment explanation


    Indices: 1513--1546  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1503 TTCGGTGACC

                        *    
       1513 CTCTTTTATGTATTTTT
          1 CTCTTTTATGTAATTTT

                     *       
       1530 CTCTTTTATTTAATTTT
          1 CTCTTTTATGTAATTTT

       1547 GGAATAAATA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71


Consensus pattern (17 bp):   
CTCTTTTATGTAATTTT

Found at i:1849 original size:28 final size:28

Alignment explanation


    Indices: 1775--1852  Score: 95
    Period size: 28  Copynumber: 2.8  Consensus size: 28

       1765 TTGTGTTGAT

                              *          
       1775 AATTTATATA-AAAATTAAATTAAATCAA
          1 AATTTATATATAAAATTATA-TAAATCAA

                 *                      *
       1803 AATATCATATATAAAATTATATAAATCAG
          1 AAT-TTATATATAAAATTATATAAATCAA

                         *       
       1832 AATTTATATATAATATTATAT
          1 AATTTATATATAAAATTATAT

       1853 GTTGAAAAAA


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
  28   19  0.44
  29   16  0.37
  30    8  0.19

ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40


Consensus pattern (28 bp):   
AATTTATATATAAAATTATATAAATCAA

Found at i:4416 original size:103 final size:103

Alignment explanation


    Indices: 4225--4430  Score: 252
    Period size: 103  Copynumber: 2.0  Consensus size: 103

       4215 AGCATCGAAT

                   *   * *              *     *       *  *                   
       4225 CAAGTTTTCATGATAAGTGACTTGAATATAATGGGTTTGTACCTCGTTACCAAATTTTCAAATTT
          1 CAAGTTTCCATCACAAGTGACTTGAATACAATGGATTTGTACATCATTACCAAATTTTCAAATTT

                         *    *     *     *       
       4290 ACAACATAATTATTCTAATTATCTGAACCATGTGATGA
         66 ACAACATAATTATGCTAACTATCTAAACCACGTGATGA

                                            *           *              *     
       4328 CAAGTTTCCATCACAAGTGACTTGAATACAATTGATTTGTACATTATT-CCTAAATTTTTAAATT
          1 CAAGTTTCCATCACAAGTGACTTGAATACAATGGATTTGTACATCATTACC-AAATTTTCAAATT

             *       *                             
       4392 TCCAACATAGTTATGCTAACTATCTAAACCACGTGATGA
         65 TACAACATAATTATGCTAACTATCTAAACCACGTGATGA

       4431 AACTTTTATA


Statistics
Matches: 86,  Mismatches: 16, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
 102    2  0.02
 103   84  0.98

ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37


Consensus pattern (103 bp):   
CAAGTTTCCATCACAAGTGACTTGAATACAATGGATTTGTACATCATTACCAAATTTTCAAATTT
ACAACATAATTATGCTAACTATCTAAACCACGTGATGA

Found at i:6970 original size:13 final size:13

Alignment explanation


    Indices: 6952--6977  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6942 AAACTAAGAA

                         
       6952 TGATCGATCGAAT
          1 TGATCGATCGAAT

                         
       6965 TGATCGATCGAAT
          1 TGATCGATCGAAT

       6978 GCAGTAAAGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31


Consensus pattern (13 bp):   
TGATCGATCGAAT

Found at i:9212 original size:2 final size:2

Alignment explanation


    Indices: 9205--9237  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       9195 GCTTGAACAT

                                                             
       9205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       9238 TAATTTATGC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.